1.

Molecular evolution

Principle: in evolution new structures (genes, organs, etc) arise only from existing ones
 2.

Origin of new genes

1. Exon duplication
2. Exon shuffling
DNA doubling
3. Gene duplication Reverse transcription
4. de novo generation: extremely rare event
5. Duplication of genome and genome segments
 3.

Exon duplication
gene
E1 E2 E3

E = exon
 3.

Exon duplication
gene
E1 E2 E2’ E3

E = exon
 4.

Exon shuffling
gene 1
E1 E2 E3
E3 E4

gene 2
E1 E2 E3

E = exon
 4.

Exon shuffling
gene 1
E1 E2 E3 E4

gene 2
E1 E2 E3 E4

E = exon
 4.

Exon shuffling
 5.

Gene duplication

chromosome
gene
gene 12
 6.

…., followed by functional

divergence
chromosome
gene 1 gene 2
 7.

The fate of new gene

Pseudogene formation

Mutations in the coding region→ pseudogene formation

X
loss-of-function

New function
(neo-functionalization)

Mutations in the coding region → new function

paralogous genes

Diverged function
(sub-functionalization)

Mutations in the regulatory regions → cell-specific gene expression

paralogous genes
 8.
Evolution of globin superfamily heme
2 chain ancient globin
1 chain ~800MY

~550MY
~500MY
~450MY
Fe
1 chain 2 chain heme

~200MY
~150MY

neuroglobin cytoglobin mioglobin

Hemoglobins (HB)
 9.

de novo origin of genes

Dissostichus Very rare

Trypsinogen

AGFP (anti-freeze glycoprotein)

Thr-Ala-Ala triplets
 10.
Duplication of higher genetic units
- Chromosomal segment duplications
- Chromosome duplication (aneuploidia)
irregular meiosis
- Whole genome duplication (poliploidia)

Other Cephalo- Unicellular

vertebrates Fishes Agnatha Insects
Entire or chordata eukaryotes

partial ploidia

ation
c
pl i
rd du
3
2nd duplication
1st duplication

Recent genome duplications:

Ancestor: 6 chromosomes - fishes, frogs, cereals
 11.
Whole genome duplication

diploid
Whole genome duplication

tetraploid
Gene loss and diploidization

diploid
Whole genome duplication

tetraploid

Gene loss and diploidization

diploid
 12.
The Hox genes
 13.
Exchange of chromosomal segments

mouse

human
 14.
Evolutionary developmental biology
(evo-devo) – evolution of genetic regulation
Sean B. Carroll
1. Evolution of regulatory regions
 Gene function is the same even in large evolutionary distances
- several genes of fruit fly and mouse are inter-changeable

 Genetic regulation, not genes, changes during evolution

- the same genes switch at different time and tissues, and are produced at different levels

2. Evolution of transcription factors

Harry Garner ésJohn W. Fondon

 Changes of amino acid content of transcription factors result

morphological changes
The length of alanine + glutamine repeats varies
 15.

Horizontal gene transfer

- Bacteria, viruses: huge gene exchange market

- Eukaryotes: no horizontal gene transfer

Vertical gene transfer : parent  offspring

Horizontal gene transfer: between non-related individuals
 16.
Molecular phylogenetic tree
Nuclear DNA
1. Genes
- Changes at silent positions
- Changes at non-silent positions

2. Non-coding DNAs

Mitochondrial and

Y chromosomal DNAs
 17.

Molecular clock

Assumption:
nucleotides of a certain DNA region change at the same speed across large periods
 18a.
Types of inheritance - reminder
 18b.
Types of inheritance - reminder
 19.

A mitochondrial DNA
Hyper-variable region
Cytochrome b gene

16,569 nucleotide
 20.
Y chromosome
Genes STRs

Genetic markers in the Y chromosome

Microsatellites
- consist of repeating units of 1-4 bp in length
(the number of repeats is compared)
Single nucleotide polymorphism (SNP)
- A DNA sequence variation occurring when a single
nucleotide differs between individuals

Molecular clock
- Sequence comparison

STR: short tandem repeats

 21.
VNTR analysis
A and B alleles

PCR Gel electrophoresis

Primer 1 Genotype

Primer 1 Primer 2

Primer 2
 Mitochondrial Eve 22.
The female whose mitochondria were inherited
by every today’s living females

How is it possible?
1. The number of human population decreased – bottle neck effect
Lived 120-150 y ago, in East Africa2. Many people lived at that time, but only a single population
(not every human population has been
analyzed  she lived may be earlier survived in the long run
- mitochondria of the surviving population, except one, have been
lost by chance (not their genomial DNAs!)

CRITICS:
rarely, mitochondria of sperm also contribute to the offspring’s mitochondrial genome  they can recombine
 23.

Y chromosomal Adam
The male whose Y chromosome is inherited by all today’s living males

He lived 60 – 90,00 years before (not at the same time as mitochondrial Eve)
- molecular clock and genetic marker studies
 24.
time: 0
The ISLAND
example – only males are indicated

7 White

4 Black

4 Tailor

9 Smith

1 Steinbacher
 24.
time: 1
The ISLAND

9 White

2 Black

5 Tailor

8 Smith

0 Steinbacher
 24.
time: 2
The ISLAND

12 White

0 Black

1 Tailor

12 Smith

0 Steinbacher
 24.
time: 3
The ISLAND

6 White

0 Black

0 Tailor

17 Smith

0 Steinbacher
 24.
time: 4
The ISLAND

2 White

0 Black

0 Tailor

21 Smith

0 Steinbacher
 24.
time:5
The ISLAND
SMITHLAND

0 White

0 Black

0 Tailor

23 Smith

0 Steinbacher